Is it biofilm or just precipitated bacteria? B subtilis is aerobic and I would expect it to grow more as a surface film (which is probably where the biofilm is more likely to form) than at the bottom of the micro titre plate well.

If Bacillus subtilis formed a biofilm due to poor agitation and prolonged growth, especially if sporulation has occurred, it may adhere to the container. For removal:

Aspiration: Use a pipette to gently aspirate the biofilm.

Scraping: A loop or cell scraper can also be used to detach the biofilm.

For more robust biofilms, consider sonication or Enzymatic treatment (these two treatments can reduce cell viability).